From de935b20e182c9ae53d365f4d02cb5a3b9a356f2 Mon Sep 17 00:00:00 2001
From: Tiago Freitas Pereira <tiagofrepereira@gmail.com>
Date: Thu, 19 Mar 2020 18:49:36 +0100
Subject: [PATCH] Handling Legacy
---
.../base/config/baselines/lda_atnt_legacy.py | 83 +++++++++++
bob/bio/base/mixins/legacy.py | 141 +++++++++++++++++-
.../pipelines/vanilla_biometrics/pipeline.py | 1 -
3 files changed, 222 insertions(+), 3 deletions(-)
create mode 100644 bob/bio/base/config/baselines/lda_atnt_legacy.py
diff --git a/bob/bio/base/config/baselines/lda_atnt_legacy.py b/bob/bio/base/config/baselines/lda_atnt_legacy.py
new file mode 100644
index 00000000..76e859cd
--- /dev/null
+++ b/bob/bio/base/config/baselines/lda_atnt_legacy.py
@@ -0,0 +1,83 @@
+# from bob.bio.base.pipelines.vanilla_biometrics.legacy import DatabaseConnector, AlgorithmAdaptor
+
+import bob.db.atnt
+from bob.bio.base.pipelines.vanilla_biometrics.legacy import DatabaseConnector
+
+database = DatabaseConnector(bob.db.atnt.Database(), protocol="Default")
+
+from sklearn.pipeline import Pipeline, make_pipeline
+from sklearn.decomposition import PCA
+
+from bob.pipelines.mixins import CheckpointMixin, SampleMixin
+from bob.bio.base.mixins import CheckpointSampleLinearize
+from bob.bio.base.mixins.legacy import LegacyProcessorMixin, LegacyAlgorithmMixin
+
+
+class CheckpointSamplePCA(CheckpointMixin, SampleMixin, PCA):
+ """
+ Enables SAMPLE and CHECKPOINTIN handling for https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html
+ """
+
+ pass
+
+
+#### PREPROCESSOR LEGACY ###
+import functools
+
+# Cropping
+CROPPED_IMAGE_HEIGHT = 80
+CROPPED_IMAGE_WIDTH = CROPPED_IMAGE_HEIGHT * 4 // 5
+
+# eye positions for frontal images
+RIGHT_EYE_POS = (CROPPED_IMAGE_HEIGHT // 5, CROPPED_IMAGE_WIDTH // 4 - 1)
+LEFT_EYE_POS = (CROPPED_IMAGE_HEIGHT // 5, CROPPED_IMAGE_WIDTH // 4 * 3)
+
+
+# RANDOM EYES POSITIONS
+# I JUST MADE UP THESE NUMBERS
+FIXED_RIGHT_EYE_POS = (30, 30)
+FIXED_LEFT_EYE_POS = (20, 50)
+import bob.bio.face
+
+face_cropper = functools.partial(
+ bob.bio.face.preprocessor.FaceCrop,
+ cropped_image_size=(CROPPED_IMAGE_HEIGHT, CROPPED_IMAGE_WIDTH),
+ cropped_positions={"leye": LEFT_EYE_POS, "reye": RIGHT_EYE_POS},
+ fixed_positions={"leye": FIXED_LEFT_EYE_POS, "reye": FIXED_RIGHT_EYE_POS},
+)
+
+from bob.pipelines.mixins import mix_me_up
+preprocessor = mix_me_up((CheckpointMixin, SampleMixin), LegacyProcessorMixin)
+
+#### ALGORITHM LEGACY #####
+
+algorithm = functools.partial(bob.bio.base.algorithm.LDA, use_pinv=True, pca_subspace_dimension=0.90)
+
+from bob.pipelines.mixins import dask_it
+
+extractor = Pipeline(
+ steps=[
+ ("0", preprocessor(callable=face_cropper, features_dir="./example/extractor0")),
+ ("1", CheckpointSampleLinearize(features_dir="./example/extractor1")),
+ (
+ "2",
+ LegacyAlgorithmMixin(
+ callable=algorithm, features_dir="./example/extractor2", model_path="./example/"
+ ),
+ ),
+ ]
+)
+# extractor = dask_it(extractor)
+
+from bob.bio.base.pipelines.vanilla_biometrics.biometric_algorithm import (
+ Distance,
+ BiometricAlgorithmCheckpointMixin,
+)
+
+
+class CheckpointDistance(BiometricAlgorithmCheckpointMixin, Distance):
+ pass
+
+
+algorithm = CheckpointDistance(features_dir="./example/")
+# algorithm = Distance()
diff --git a/bob/bio/base/mixins/legacy.py b/bob/bio/base/mixins/legacy.py
index 3c3cc470..6f34efc6 100644
--- a/bob/bio/base/mixins/legacy.py
+++ b/bob/bio/base/mixins/legacy.py
@@ -8,9 +8,33 @@ Mixins to handle legacy components
"""
from bob.pipelines.mixins import CheckpointMixin, SampleMixin
-from sklearn.base import TransformerMixin
+from sklearn.base import TransformerMixin, BaseEstimator
from sklearn.utils.validation import check_array
+from bob.pipelines.sample import Sample, DelayedSample, SampleSet
+import numpy
+import logging
+import os
+logger = logging.getLogger(__name__)
+def scikit_to_bob_supervised(X, Y):
+ """
+ Given an input data ready for :py:method:`scikit.estimator.BaseEstimator.fit`,
+ convert for :py:class:`bob.bio.base.algorithm.Algorithm.train_projector` when
+ `performs_projection=True`
+ """
+
+ # TODO: THIS IS VERY INNEFICI
+ logger.warning("INEFFICIENCY WARNING. HERE YOU ARE USING A HACK FOR USING BOB ALGORITHMS IN SCIKIT LEARN PIPELINES. \
+ WE RECOMMEND YOU TO PORT THIS ALGORITHM. DON'T BE LAZY :-)")
+
+ bob_output = dict()
+ for x,y in zip(X, Y):
+ if y in bob_output:
+ bob_output[y] = numpy.vstack((bob_output[y], x.data))
+ else:
+ bob_output[y] = x.data
+
+ return [bob_output[k] for k in bob_output]
class LegacyProcessorMixin(TransformerMixin):
"""Class that wraps :py:class:`bob.bio.base.preprocessor.Preprocessor` and
@@ -41,7 +65,8 @@ class LegacyProcessorMixin(TransformerMixin):
"""
- def __init__(self, callable=None):
+ def __init__(self, callable=None, **kwargs):
+ super().__init__(**kwargs)
self.callable = callable
self.instance = None
@@ -56,3 +81,115 @@ class LegacyProcessorMixin(TransformerMixin):
if self.instance is None:
self.instance = self.callable()
return [self.instance(x) for x in X]
+
+
+from bob.pipelines.mixins import CheckpointMixin, SampleMixin
+class LegacyAlgorithmMixin(CheckpointMixin,SampleMixin,BaseEstimator):
+ """Class that wraps :py:class:`bob.bio.base.algorithm.Algoritm` and
+
+ LegacyAlgorithmrMixin.fit maps :py:method:`bob.bio.base.algorithm.Algoritm.train_projector`
+
+ LegacyAlgorithmrMixin.transform maps :py:method:`bob.bio.base.algorithm.Algoritm.project`
+
+ THIS HAS TO BE SAMPABLE AND CHECKPOINTABLE
+
+
+ Example
+ -------
+
+ Wrapping preprocessor with functtools
+ >>> from bob.bio.base.mixins.legacy import LegacyProcessorMixin
+ >>> from bob.bio.face.preprocessor import FaceCrop
+ >>> import functools
+ >>> transformer = LegacyProcessorMixin(functools.partial(FaceCrop, cropped_image_size=(10,10)))
+
+ Example
+ -------
+ Wrapping extractor
+ >>> from bob.bio.base.mixins.legacy import LegacyProcessorMixin
+ >>> from bob.bio.face.extractor import Linearize
+ >>> transformer = LegacyProcessorMixin(Linearize)
+
+
+ Parameters
+ ----------
+ callable: callable
+ Calleble function that instantiates the scikit estimator
+
+ """
+
+ def __init__(self, callable=None, **kwargs):
+ super().__init__(**kwargs)
+ self.callable = callable
+ self.instance = None
+ self.projector_file = os.path.join(self.model_path, "Projector.hdf5")
+
+ def fit(self, X, y=None, **fit_params):
+
+ if os.path.exists(self.projector_file):
+ return self
+
+ # Instantiates and do the "real" fit
+ if self.instance is None:
+ self.instance = self.callable()
+
+ if self.instance.performs_projection:
+ # Organizing the date by class
+ bob_X = scikit_to_bob_supervised(X, y)
+ self.instance.train_projector(bob_X, self.projector_file)
+ else:
+ self.instance.train_projector(X, **fit_params)
+
+ # Deleting the instance, so it's picklable
+ self.instance = None
+
+ return self
+
+ def transform(self, X):
+
+ if not isinstance(X, list):
+ raise ValueError("It's expected a list, not %s" % type(X))
+
+ # Instantiates and do the "real" transform
+ if self.instance is None:
+ self.instance = self.callable()
+ self.instance.load_projector(self.projector_file)
+
+ import ipdb; ipdb.set_trace()
+
+ if isinstance(X[0], Sample) or isinstance(X[0], DelayedSample):
+ #samples = []
+ for s in X:
+ projected_data = self.instance.project(s.data)
+
+ #raw_X = [s.data for s in X]
+ elif isinstance(X[0], SampleSet):
+
+ sample_sets = []
+ for sset in X:
+
+ samples = []
+ for sample in sset.samples:
+
+ # Project
+ projected_data = self.instance.project(sample.data)
+
+ #Checkpointing
+ path = self.make_path(sample)
+ self.instance.write_feature(path)
+
+ samples.append(DelayedSample())
+
+
+ pass
+ #bob.io.base.save(projected_data)
+
+
+
+
+ #raw_X = [x.data for s in X for x in s.samples]
+ else:
+ raise ValueError("Type not allowed %s" % type(X[0]))
+
+
+ return self.instance.project(raw_X)
diff --git a/bob/bio/base/pipelines/vanilla_biometrics/pipeline.py b/bob/bio/base/pipelines/vanilla_biometrics/pipeline.py
index 06d891a8..5ce6e673 100644
--- a/bob/bio/base/pipelines/vanilla_biometrics/pipeline.py
+++ b/bob/bio/base/pipelines/vanilla_biometrics/pipeline.py
@@ -54,7 +54,6 @@ def train_background_model(background_model_samples, extractor):
def create_biometric_reference(
biometric_reference_samples, extractor, biometric_algorithm
):
-
biometric_reference_features = extractor.transform(biometric_reference_samples)
# TODO: I KNOW THIS LOOKS UGLY, BUT THIS `MAP_PARTITIONS` HAS TO APPEAR SOMEWHERE
--
GitLab